MultiQC Report

v1.29

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If you use plots from MultiQC in a publication or presentation, please cite:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.29

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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General Statistics

Showing ¹²/₁₂ rows and ²/₄ columns.

Sample Name	Reads	Reads mapped	% Reads mapped	% Aligned
SRR4420293_flagstat	51.4M	50.2M	97.6%
SRR4420293_hisat2				96.3%
SRR4420294_flagstat	135.3M	133.2M	98.4%
SRR4420294_hisat2				97.2%
SRR4420295_flagstat	49.6M	48.3M	97.5%
SRR4420295_hisat2				96.0%
SRR4420296_flagstat	47.5M	44.5M	93.7%
SRR4420296_hisat2				92.7%
SRR4420297_flagstat	68.6M	66.9M	97.6%
SRR4420297_hisat2				96.1%
SRR4420298_flagstat	74.5M	73.0M	98.0%
SRR4420298_hisat2				96.7%

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools: flagstat	Reads	Total reads in the bam file (millions)	`samtools_flagstat-flagstat_total`	read_count
\|\|	Samtools: flagstat	Reads mapped	Reads mapped in the bam file (millions)	`samtools_flagstat-mapped_passed`	read_count
\|\|	Samtools: flagstat	% Reads mapped	% Reads mapped in the bam file	`samtools_flagstat-mapped_passed_pct`
\|\|	Bowtie 2 / HiSAT2	% Aligned	overall alignment rate	`bowtie_2_hisat2-overall_alignment_rate`

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
SRR4420293_flagstat	51.4M	51.4M	50.2M	18.5M	0.0M	32.9M	30.6M	31.0M	0.7M	0.2M	0.1M
SRR4420294_flagstat	135.3M	135.3M	133.2M	59.3M	0.0M	76.0M	71.2M	72.4M	1.5M	0.5M	0.1M
SRR4420295_flagstat	49.6M	49.6M	48.3M	17.7M	0.0M	31.9M	29.2M	29.9M	0.8M	0.4M	0.1M
SRR4420296_flagstat	47.5M	47.5M	44.5M	6.7M	0.0M	40.9M	36.7M	37.1M	0.8M	0.1M	0.0M
SRR4420297_flagstat	68.6M	68.6M	66.9M	25.9M	0.0M	42.7M	39.7M	40.2M	0.8M	0.2M	0.1M
SRR4420298_flagstat	74.5M	74.5M	73.0M	29.4M	0.0M	45.1M	42.0M	42.7M	0.9M	0.3M	0.1M

Sort	Column	Description	ID	Scale
\|\|	Total Reads	Total Reads	`flagstat_total`	read_count
\|\|	Total Passed QC	Total Passed QC	`total_passed`	read_count
\|\|	Mapped	Mapped	`mapped_passed`	read_count
\|\|	Secondary Alignments	Secondary Alignments	`secondary_passed`	read_count
\|\|	Duplicates	Duplicates	`duplicates_passed`	read_count
\|\|	Paired in Sequencing	Paired in Sequencing	`paired_in_sequencing_passed`	read_count
\|\|	Properly Paired	Properly Paired	`properly_paired_passed`	read_count
\|\|	Self and mate mapped	Reads with itself and mate mapped	`with_itself_and_mate_mapped_passed`	read_count
\|\|	Singletons	Singletons	`singletons_passed`	read_count
\|\|	Mate mapped to diff chr	Mate mapped to different chromosome	`with_mate_mapped_to_a_different_chr_passed`	read_count
\|\|	Diff chr (mapQ >= 5)	Mate mapped to different chromosome (mapQ >= 5)	`with_mate_mapped_to_a_different_chr_mapQ_5__passed`	read_count

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
SRR4420293_flagstat	100.0%	100.0%	97.6%	35.9%	0.0%	64.1%	59.5%	60.4%	1.3%	0.4%	0.2%
SRR4420294_flagstat	100.0%	100.0%	98.4%	43.8%	0.0%	56.2%	52.6%	53.5%	1.1%	0.4%	0.1%
SRR4420295_flagstat	100.0%	100.0%	97.4%	35.6%	0.0%	64.4%	59.0%	60.3%	1.6%	0.7%	0.3%
SRR4420296_flagstat	100.0%	100.0%	93.7%	14.0%	0.0%	86.0%	77.3%	78.0%	1.6%	0.1%	0.1%
SRR4420297_flagstat	100.0%	100.0%	97.6%	37.8%	0.0%	62.2%	57.9%	58.7%	1.1%	0.4%	0.1%
SRR4420298_flagstat	100.0%	100.0%	98.0%	39.5%	0.0%	60.5%	56.4%	57.3%	1.2%	0.5%	0.1%

Sort	Column	Description	ID
\|\|	Total Reads	Total Reads	`flagstat_total_pct`
\|\|	Total Passed QC	Total Passed QC	`total_passed_pct`
\|\|	Mapped	Mapped	`mapped_passed_pct`
\|\|	Secondary Alignments	Secondary Alignments	`secondary_passed_pct`
\|\|	Duplicates	Duplicates	`duplicates_passed_pct`
\|\|	Paired in Sequencing	Paired in Sequencing	`paired_in_sequencing_passed_pct`
\|\|	Properly Paired	Properly Paired	`properly_paired_passed_pct`
\|\|	Self and mate mapped	Self and mate mapped	`with_itself_and_mate_mapped_passed_pct`
\|\|	Singletons	Singletons	`singletons_passed_pct`
\|\|	Mate mapped to diff chr	Mate mapped to diff chr	`with_mate_mapped_to_a_different_chr_passed_pct`
\|\|	Diff chr (mapQ >= 5)	Diff chr (mapQ >= 5)	`with_mate_mapped_to_a_different_chr_mapQ_5__passed_pct`

v1.29

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